Nucleosome reassembly at the TSS is the initiating event in <i>MLH1</i> resilencing.

<p><b>A</b>, Regions assayed for nucleosome occupancy using MNase-qPCR (Regions I–IX) and NOMe-Seq (Regions N1 and N2). Shown beneath the gene schematic is NOMe-Seq data from untreated RKO cells at Region N1. Black arrows indicate the <i>MLH1</i> and <i>EPM2AIP1</i> TSS. Bottom panel represents GpC accessibility. Black circles = GpC dinucleotides methylated/accessible to the GpC methyltransferase M.<i>Cvi</i>PI. White circles = GpC dinucleotides not methylated/inaccessible to GpC methyltransferase. Pink shading indicates regions of inaccessibility of ≥150 bp. Asterix = region of M.<i>Cvi</i>PI accessibility. <b>B</b>, Relative nucleosome levels in untreated RKO cells at the indicated regions (black bars labeled Regions I–IX) as determined by MNase-qPCR. Drawn to scale with schematic shown in A. Error bars = SD. <b>C</b> and <b>D</b>, qPCR results showing changes in relative nucleosome levels at Regions III and VI following decitabine exposure. <b>E</b> and <b>F</b>, <i>MLH1</i> gene expression (E) and promoter bisulfite pyrosequencing (F), reproduced from <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003636#pgen-1003636-g002" target="_blank">Figure 2A and D</a> for ease of comparison with nucleosome levels. <b>G–I</b>, NOMe-Seq analysis of the <i>MLH1</i> promoter at Region N2 in SW620 (F) and RKO (G,H) cells at the indicated treatment points. Black filled triangles = methylated CpG dinucleotides; white filled triangles = unmethylated CpG dinucleotides. See also <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003636#pgen.1003636.s002" target="_blank">Figure S2</a>.